Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model

Bioinformatics
Miquel Marin-RieraIsaac Salazar-Ciudad

Abstract

The transformation of the embryo during development requires complex gene networks, cell signaling and gene-regulated cell behaviors (division, adhesion, polarization, apoptosis, contraction, extracellular matrix secretion, signal secretion and reception, etc.). There are several models of development implementing these phenomena, but none considers at the same time the very different bio-mechanical properties of epithelia, mesenchyme, extracellular matrix and their interactions. Here, we present a new computational model and accompanying open-source software, EmbryoMaker, that allows the user to simulate custom developmental processes by designing custom gene networks capable of regulating cell signaling and all animal basic cell behaviors. We also include an editor to implement different initial conditions, mutations and experimental manipulations. We show the applicability of the model by simulating several complex examples of animal development. The source code can be downloaded from: http://www.biocenter.helsinki.fi/salazar/software.html. isalazar@mappi.helsinki.fi Supplementary data are available at Bioinformatics online.

References

Oct 21, 1991·Journal of Theoretical Biology·E MjolsnessJ Reinitz
Jun 21, 1990·Journal of Theoretical Biology·F W Cummings
Sep 28, 1992·Physical Review Letters·F Graner, J A Glazier
May 17, 2002·Current Biology : CB·Eli MeirGarrett M Odell
Apr 2, 2003·Development·Isaac Salazar-CiudadStuart A Newman
Feb 7, 2004·Bioinformatics·J A IzaguirreJ A Glazier
Aug 13, 2004·Proceedings. Biological Sciences·H G E HentschelStuart A Newman
Dec 31, 2005·Physical Review Letters·Adrian NeaguGabor Forgacs
Nov 21, 2007·Current Topics in Developmental Biology·Isaac Salazar-Ciudad
Dec 18, 2007·Current Biology : CB·Reza FarhadifarFrank Jülicher
Apr 12, 2008·Physical Biology·Sebastian A Sandersius, Timothy J Newman
Mar 12, 2010·Nature·Isaac Salazar-Ciudad, Jukka Jernvall
Jul 1, 2005·Mathematical Biosciences and Engineering : MBE·T J Newman
Dec 15, 2010·Plant Physiology·Roeland M H MerksGerrit T S Beemster
Feb 8, 2011·Cell·Nicolas MincFred Chang
Sep 8, 2011·Journal of Mathematical Biology·Aaron M SmithPhilip K Maini
Feb 4, 2014·Seminars in Cell & Developmental Biology·Leah C Biggs, Marja L Mikkola
Jul 24, 2014·Development·Jacqueline E Moustakas-VerhoScott F Gilbert
Mar 15, 2015·Bioinformatics·Simon TanakaDagmar Iber

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Citations

Nov 27, 2016·Development·Miguel Brun-UsanIsaac Salazar-Ciudad
Mar 30, 2017·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Alexander G FletcherRuth E Baker
Oct 9, 2019·Frontiers in Genetics·Sandra Montes-OlivasMartin Homer
Oct 20, 2019·Development·Pascal F HagolaniIsaac Salazar-Ciudad
Nov 20, 2020·Physical Biology·Nicola Mulberry, Leah Edelstein-Keshet
Mar 13, 2020··Raymond SpiteriMaurice Hendrix

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